There are many provisions that can cause this. Some States have you report the entire amount; some only want the amount earned when there was a physical presence in that State, or only if the company having you work remotely is in that State, even if you are not. Or, there is some payout that qualifies for exclusion or exemption for the State but not the Feds (Worker comp, third-party sick pay, retirement, some sort of incentive program, some taxable-nontaxable fringe benefit) or vice versa. Or, there is more than one State, and you never try to make the State amounts total 100%, for some of these same reasons.

You would have to give more details, and did you ask the taxpayer about this? Sometimes they'll respond with, "Oh, yeah, about that..."